Modulating plant nitrogen levels

ABSTRACT

Methods and materials for modulating (e.g., increasing or decreasing) nitrogen levels in plants are disclosed. For example, nucleic acids encoding nitrogen-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Plants and plant products having increased nitrogen levels are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 11/292,951, filed Dec. 2, 2005, which claims priority under 35 U.S.C. §119 to U.S. Provisional Application No. 60/705,119, filed Aug. 2, 2005, and to U.S. Provisional Application No. 60/637,311, filed Dec. 16, 2004. The disclosures of the prior applications are considered part of (and are incorporated by reference in) the disclosure of this application.

TECHNICAL FIELD

This document provides methods and materials related to modulating (e.g., increasing or decreasing) nitrogen levels in plants. For example, this document provides plants having increased nitrogen levels as well as materials and methods for making plants and plant products having increased nitrogen levels.

BACKGROUND

The photoautotrophic production of organic nitrogenous compounds is crucial to plant metabolism, growth, and development. Protein and amino acid contents of harvested plant materials are of great agronomic importance in many crop species. Light-driven nitrogen (N) assimilation in leaves has evolved to operate alongside and integrate with photosynthesis and respiration. The production of reduced carbon (C) in photosynthesis and its reoxidation in respiration are necessary to produce both the energy and C skeletons required for the incorporation of inorganic N into amino acids. Conversely, N assimilation is required to sustain the output of organic C and N. This network is further complicated by the concomitant operation of photorespiratory metabolism. Both the rate of N assimilation and the coordination of C and N assimilation are under multifactorial control by a repertoire of signals, which provide information on C and N status. There is a need for compositions and methods that can increase nitrogen content in plants under varying nitrogen conditions.

SUMMARY

This document provides methods and materials related to plants having modulated (e.g., increased or decreased) nitrogen content. For example, this document provides transgenic plants and plant cells having increased levels of nitrogen, nucleic acids used to generate transgenic plants and plant cells having increased levels of nitrogen, and methods for making plants and plant cells having increased levels of nitrogen. Such plants and plant cells can be grown to produce seeds having increased nitrogen content. The seeds may be used to produce foodstuffs and animal feed having increased nutritional (e.g., protein) content, which may benefit both food producers and consumers. While not being bound to any particular mode of action, the nitrogen-modulating polypeptides provided herein may have activities as transport proteins. For example, the polypeptides provided herein may be involved in transport of nitrogen, e.g., organic nitrogen in the form of peptides or amino acids, or inorganic nitrogen in the form of ammonium or nitrate.

In one embodiment, a method of modulating the level of nitrogen in a plant is provided. The method comprises introducing into a plant cell an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NOs:4-18, and the consensus sequence set forth in FIG. 1, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In another embodiment, a method of modulating the level of nitrogen in a plant is provided. The method comprises introducing into a plant cell an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:16, and the consensus sequence set forth in FIG. 1, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In a further embodiment, a method of modulating the level of nitrogen in a plant is provided. The method comprises introducing into a plant cell an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:16, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

The sequence identity can be 85 percent or greater, 90 percent or greater, or 95 percent or greater. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:2. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:4. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to the consensus sequence set forth in FIG. 1. The difference can be an increase in the level of nitrogen.

The isolated nucleic acid can be operably linked to a regulatory region. The regulatory region can be a tissue-specific regulatory region. The tissue-specific regulatory region can be a promoter. The promoter can be selected from the group consisting of YP0092, PT0676, PT0708, the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene, the soybean α subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, and the barley hordein gene promoter. The promoter can be selected from the group consisting of PT0613, PT0672, PT0678, PT0688, PT0837, YP0128, YP0275, PT0625, PT0660, PT0683, and PT0758. The regulatory region can be a broadly expressing promoter. The broadly expressing promoter can be selected from the group consisting of p13879, p32449, 21876, p326, YP0158, YP0214, YP0380, PT0848, PT0633, YP0050, YP0144, and YP0190. The regulatory region can be an inducible promoter.

The plant can be a dicot. The plant can be a member of the genus Brassica, Glycine, Gossypiurn, Helianthus, Lactuca, Lycopersicon, Solanum, Vitis, Pisum, Medicago, Carthamus, Arachis, Olea, Linum, or Trifolium. The plant can be a monocot. The plant can be a member of the genus Zea, Triticum, Hordeum, Secale, Oryza, Triticosecale, Avena, Musa, Elaeis, Phleum, or Sorghum. The tissue can be seed tissue.

A method of producing a plant tissue is also provided. The method comprises growing a plant cell comprising an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NOs:4-18, and the consensus sequence set forth in FIG. 1, where the tissue has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In another embodiment, a method of producing a plant tissue is provided. The method comprises growing a plant cell comprising an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:16, and the consensus sequence set forth in FIG. 1, where the tissue has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In yet another embodiment, a method of producing a plant tissue is provided. The method comprises growing a plant cell comprising an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:16, where the tissue has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

The sequence identity can be 85 percent or greater, 90 percent or greater, or 95 percent or greater. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:2. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:4. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to the consensus sequence set forth in FIG. 1. The difference can be an increase in the level of nitrogen.

The isolated nucleic acid can be operably linked to a regulatory region. The regulatory region can be a tissue-specific regulatory region. The tissue-specific regulatory region can be a promoter. The promoter can be selected from the group consisting of YP0092, PT0676, PT0708, the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene, the soybean α subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, and the barley hordein gene promoter. The promoter can be selected from the group consisting of PT0613, PT0672, PT0678, PT0688, PT0837, YP0128, YP0275, PT0625, PT0660, PT0683, and PT0758. The regulatory region can be a broadly expressing promoter. The broadly expressing promoter can be selected from the group consisting of p13879, p32449, 21876, p326, YP0158, YP0214, YP0380, PT0848, PT0633, YP0050, YP0144, and YP0190. The regulatory region can be an inducible promoter.

The plant tissue can be dicotyledonous. The plant tissue can be a member of the genus Brassica, Glycine, Gossypium, Helianthus, Lactuca, Lycopersicon, Solanum, Vitis, Pisum, Medicago, Carthamus, Arachis, Olea, Linum, or Trifolium. The plant tissue can be monocotyledonous. The plant tissue can be a member of the genus Zea, Triticum, Hordeum, Secale, Oryza, Triticosecale, Avena, Musa, Elaeis, Phleum, or Sorghum. The tissue can be seed tissue.

A plant cell is also provided. The plant cell comprises an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NOs:4-18, and the consensus sequence set forth in FIG. 1, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In another embodiment, a plant cell is provided. The plant cell comprises an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:16, and the consensus sequence set forth in FIG. 1, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

In yet another embodiment, a plant cell is provided. The plant cell comprises an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:16, where a tissue of a plant produced from the plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise the nucleic acid.

The sequence identity can be 85 percent or greater, 90 percent or greater, or 95 percent or greater, The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:2. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to SEQ ID NO:4. The nucleotide sequence can encode a polypeptide comprising an amino acid sequence corresponding to the consensus sequence set forth in FIG. 1. The difference can be an increase in the level of nitrogen.

The isolated nucleic acid can be operably linked to a regulatory region. The regulatory region can be a tissue-specific regulatory region. The tissue-specific regulatory region can be a promoter. The promoter can be selected from the group consisting of YP0092, PT0676, PT0708, the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene, the soybean α subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, and the barley hordein gene promoter. The promoter can be selected from the group consisting of PT0613, PT0672, PT0678, PT0688, PT0837, YP0128, YP0275, PT0625, PT0660, PT0683, and PT0758. The regulatory region can be a broadly expressing promoter. The broadly expressing promoter can be selected from the group consisting of p13879, p32449, 21876, p326, YP0158, YP0214, YP0380, PT0848, PT0633, YP0050, YP0144, and YP0190. The regulatory region can be an inducible promoter.

The plant can be a dicot. The plant can be a member of the genus Brassica, Glycine, Gossypium, Helianthus, Lactuca, Lycopersicon, Solanum, Vitis, Pisum, Medicago, Carthamus, Arachis, Olea, Linum, or Trifolium. The plant can be a monocot. The plant can be a member of the genus Zea, Triticum, Hordeum, Secale, Oryza, Triticosecale, Avena, Musa, Elaeis, Phleum, or Sorghum. The tissue can be seed tissue.

A transgenic plant is also provided. The transgenic plant comprises any of the plant cells described above. Progeny of the transgenic plant are also provided. The progeny have a difference in the level of nitrogen as compared to the level of nitrogen in a corresponding control plant that does not comprise the isolated nucleic acid. Seed and vegetative tissue from the transgenic plant are also provided. In addition, food products and feed products comprising vegetative tissue from the transgenic plant are provided.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1G are an alignment of SEQ ID NO:4 with orthologous amino acid sequences SEQ ID NOs:5-7, SEQ ID NOs:9-12, SEQ ID NO:14, and SEQ ID NOs:16-18. The consensus sequence determined by the alignment is set forth.

DETAILED DESCRIPTION

This invention features methods and materials related to plants, plant products, plant tissues, and plant cells having modulated (e.g., increased or decreased) levels of nitrogen. For example, this document provides plants and plant cells having increased nitrogen levels as well as methods for producing such plants and plant cells. The methods can include transforming a plant cell with a nucleic acid encoding a nitrogen-modulating polypeptide, wherein expression of the polypeptide results in increased levels of nitrogen. Plants and plant cells produced using such methods can be grown to produce seeds having increased nitrogen levels. The seeds may be used to produce foodstuffs and animal feed having increased nutritional (e.g., protein) content, which may benefit both food producers and consumers.

Polypeptides

The term “polypeptide” as used herein refers to a compound of two or more subunit amino acids, amino acid analogs, or other peptidomimetics, regardless of post-translational modification, e.g., phosphorylation or glycosylation. The subunits may be linked by peptide bonds or other bonds such as, for example, ester or ether bonds. The term “amino acid” refers to natural and/or unnatural or synthetic amino acids, including D/L optical isomers. Full-length proteins, analogs, mutants, and fragments thereof are encompassed by this definition.

Described herein are nitrogen-modulating polypeptides. Nitrogen-modulating polypeptides can be effective to modulate nitrogen levels when expressed in a plant or plant cell. Modulation of the level of nitrogen can be either an increase or a decrease in the level of nitrogen relative to the corresponding level in a control plant. A nitrogen-modulating polypeptide can be a transporter polypeptide, such as an oligopeptide transporter polypeptide.

A nitrogen-modulating polypeptide can be a proton-dependent oligopeptide transport (POT) family polypeptide. POT family polypeptides are reported to be involved in the intake of small peptides with the concomitant uptake of a proton. SEQ ID NO:2 and SEQ ID NO:4 set forth the amino acid sequences of Arabidopsis clones, identified herein as Ceres cDNA ID 2998984 (SEQ ID NO:1) and Ceres clone 117581 (SEQ ID NO:3), respectively, each of which has a PTR2 domain characteristic of a peptide transporter polypeptide.

A nitrogen-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO:4. Alternatively, a nitrogen-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO:4. For example, a nitrogen-modulating polypeptide can have an amino acid sequence with at least 40% sequence identity, e.g., 41%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO:4. In some embodiments, a nitrogen-modulating polypeptide comprises an amino acid sequence with at least 40% sequence identity to SEQ ID NO:2 and a chloroplast targeting signal sequence at the N-terminus of the polypeptide.

Amino acid sequences of orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:4 are provided in FIGS. 1A-1G, along with a consensus sequence. A consensus amino acid sequence for such orthologs was determined by aligning amino acid sequences, e.g., amino acid sequences related to SEQ ID NO:4, from a variety of species and determining the most common amino acid or type of amino acid at each position. For example, the alignment in FIG. 1 provides the amino acid sequences of Ceres clone 117581 (SEQ ID NO:4), CeresClone:328378 (SEQ ID NO:5), gi|2655098 (SEQ ID NO:6), gi|34895718 (SEQ ID NO:7), gi|4102839 (SEQ ID NO:9), gi|31088360 (SEQ ID NO:10), gi|6635838 (SEQ ID NO:11), gi|56784523 (SEQ ID NO:12), gi|50059161 (SEQ ID NO:14), CeresClone:352232 (SEQ ID NO:16), gi|33411520 (SEQ ID NO:17), and gi|31429847 (SEQ ID NO:18). Other orthologs include gi|50933627 (SEQ ID NO:8), gi|56784524 (SEQ ID NO:13), and gi|6409176 (SEQ ID NO:15).

In some cases, a nitrogen-modulating polypeptide can include a polypeptide having at least 80% sequence identity (e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity) to an amino acid sequence corresponding to SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, or the consensus sequence set forth in FIG. 1.

It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given nitrogen-modulating polypeptide can be modified such that optimal expression in a particular plant species is obtained, using appropriate codon bias tables for that species.

A nitrogen-modulating polypeptide encoded by a recombinant nucleic acid can be a native nitrogen-modulating polypeptide, i.e., one or more additional copies of the coding sequence for a nitrogen-modulating polypeptide that is naturally present in the cell. Alternatively, a nitrogen-modulating polypeptide can be heterologous to the cell, e.g., a transgenic Lycopersicon plant can contain the coding sequence for a transporter polypeptide from a Glycine plant.

A nitrogen-modulating polypeptide can include additional amino acids that are not involved in nitrogen modulation, and thus can be longer than would otherwise be the case. For example, a nitrogen-modulating polypeptide can include an amino acid sequence that functions as a reporter. Such a nitrogen-modulating polypeptide can be a fusion protein in which a green fluorescent protein (GFP) polypeptide is fused to SEQ ID NO:2, or in which a yellow fluorescent protein (YFP) polypeptide is fused to SEQ ID NO:4. In some embodiments, a nitrogen-modulating polypeptide includes a purification tag or a leader sequence added to the amino or carboxy terminus.

Nitrogen-modulating polypeptide candidates suitable for use in the invention can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify orthologs of nitrogen-modulating polypeptides. Sequence analysis can involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundant databases using known nitrogen-modulating polypeptide amino acid sequences. Those proteins in the database that have greater than 40% sequence identity can be identified as candidates for further evaluation for suitability as a nitrogen-modulating polypeptide. If desired, manual inspection of such candidates can be carried out in order to narrow the number of candidates to be further evaluated. Manual inspection can be performed by selecting those candidates that appear to have domains suspected of being present in nitrogen-modulating polypeptides, e.g., conserved functional domains.

The identification of conserved regions in a template or subject polypeptide can facilitate production of variants of wild type nitrogen-modulating polypeptides. Conserved regions can be identified by locating a region within the primary amino acid sequence of a template polypeptide that is a repeated sequence, forms some secondary structure (e.g., helices and beta sheets), establishes positively or negatively charged domains, or represents a protein motif or domain. See, e.g., the Pfam web site describing consensus sequences for a variety of protein motifs and domains at sanger.ac.uk/Pfam and genome.wustl.edu/Pfam. A description of the information included at the Pfam database is described in Sonnhammer et al., 1998, Nucl. Acids Res. 26: 320-322; Sonnhammer et al., 1997, Proteins 28:405-420; and Bateman et al., 1999, Nucl. Acids Res. 27:260-262.

Conserved regions also can be determined by aligning sequences of the same or related polypeptides from closely related species. Closely related species preferably are from the same family. In some embodiments, alignment of sequences from two different species is adequate. For example, sequences from Arabidopsis and Zea mays can be used to identify one or more conserved regions.

Typically, polypeptides that exhibit at least about 40% amino acid sequence identity are useful to identify conserved regions. Conserved regions of related polypeptides can exhibit at least 45% amino acid sequence identity (e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity). In some embodiments, a conserved region of target and template polypeptides exhibit at least 92, 94, 96, 98, or 99% amino acid sequence identity. Amino acid sequence identity can be deduced from amino acid or nucleotide sequences. In certain cases, highly conserved domains have been identified within nitrogen-modulating polypeptides. These conserved regions can be useful in identifying functionally similar (orthologous) nitrogen-modulating polypeptides.

In some instances, suitable nitrogen-modulating polypeptides can be synthesized on the basis of consensus functional domains and/or conserved regions in polypeptides that are homologous nitrogen-modulating polypeptides. Domains are groups of substantially contiguous amino acids in a polypeptide that can be used to characterize protein families and/or parts of proteins. Such domains have a “fingerprint” or “signature” that can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, domains are correlated with specific in vitro and/or in vivo activities. A domain can have a length of from 10 amino acids to 400 amino acids, e.g., 10 to 50 amino acids, or 25 to 100 amino acids, or 35 to 65 amino acids, or 35 to 55 amino acids, or 45 to 60 amino acids, or 200 to 300 amino acids, or 300 to 400 amino acids.

Consensus domains and conserved regions can be identified by homologous polypeptide sequence analysis as described above. The suitability of polypeptides for use as nitrogen-modulating polypeptides can be evaluated by functional complementation studies.

Nucleic Acids

Isolated nucleic acids are provided herein. The terms “nucleic acid” and “polynucleotide” are used interchangeably herein, and refer to both RNA and DNA, including cDNA, genomic DNA, synthetic DNA, and DNA (or RNA) containing nucleic acid analogs. Polynucleotides can have any three-dimensional structure. A nucleic acid can be double-stranded or single-stranded (i.e., a sense strand or an antisense strand). Non-limiting examples of polynucleotides include genes, gene fragments, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers, as well as nucleic acid analogs.

An isolated nucleic acid can be, for example, a naturally-occurring DNA molecule, provided one of the nucleic acid sequences normally found immediately flanking that DNA molecule in a naturally-occurring genome is removed or absent. Thus, an isolated nucleic acid includes, without limitation, a DNA molecule that exists as a separate molecule, independent of other sequences (e.g., a chemically synthesized nucleic acid, or a cDNA or genomic DNA fragment produced by the polymerase chain reaction (PCR) or restriction endonuclease treatment). An isolated nucleic acid also refers to a DNA molecule that is incorporated into a vector, an autonomously replicating plasmid, a virus, or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid can include an engineered nucleic acid such as a DNA molecule that is part of a hybrid or fusion nucleic acid. A nucleic acid existing among hundreds to millions of other nucleic acids within, for example, cDNA libraries or genomic libraries, or gel slices containing a genomic DNA restriction digest, is not to be considered an isolated nucleic acid.

Isolated nucleic acid molecules can be produced by standard techniques. For example, polymerase chain reaction (PCR) techniques can be used to obtain an isolated nucleic acid containing a nucleotide sequence described herein. PCR can be used to amplify specific sequences from DNA as well as RNA, including sequences from total genomic DNA or total cellular RNA. Various PCR methods are described, for example, in PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, eds., Cold Spring Harbor Laboratory Press, 1995. Generally, sequence information from the ends of the region of interest or beyond is employed to design oligonucleotide primers that are identical or similar in sequence to opposite strands of the template to be amplified. Various PCR strategies also are available by which site-specific nucleotide sequence modifications can be introduced into a template nucleic acid. Isolated nucleic acids also can be chemically synthesized, either as a single nucleic acid molecule (e.g., using automated DNA synthesis in the 3′ to 5′ direction using phosphoramidite technology) or as a series of oligonucleotides. For example, one or more pairs of long oligonucleotides (e.g., >100 nucleotides) can be synthesized that contain the desired sequence, with each pair containing a short segment of complementarity (e.g., about 15 nucleotides) such that a duplex is formed when the oligonucleotide pair is annealed. DNA polymerase is used to extend the oligonucleotides, resulting in a single, double-stranded nucleic acid molecule per oligonucleotide pair, which then can be ligated into a vector. Isolated nucleic acids of the invention also can be obtained by mutagenesis of, e.g., a naturally occurring DNA.

As used herein, the term “percent sequence identity” refers to the degree of identity between any given query sequence and a subject sequence. A subject sequence typically has a length that is more than 80 percent, e.g., more than 82, 85, 87, 89, 90, 93, 95, 97, 99, 100, 105, 110, 115, or 120 percent, of the length of the query sequence. A query nucleic acid or amino acid sequence is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment). Chema, et al. (2003) Nucleic Acids Res 31 (13):3497-500.

ClustalW calculates the best match between a query and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a query sequence, a subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2; window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For multiple alignment of nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg, and Lys; residue-specific gap penalties: on. The output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher site (searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at the European Bioinformatics Institute site on the World Wide Web (ebi.ac.uk/clustalw). To determine a “percent identity” between a query sequence and a subject sequence, the number of matching bases or amino acids in the alignment is divided by the total number of matched and mismatched bases or amino acids, followed by multiplying the result by 100. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2. It also is noted that the length value will always be an integer.

The term “exogenous” with respect to a nucleic acid indicates that the nucleic acid is part of a recombinant nucleic acid construct, or is not in its natural environment. For example, an exogenous nucleic acid can be a sequence from one species introduced into another species, i.e., a heterologous nucleic acid. Typically, such an exogenous nucleic acid is introduced into the other species via a recombinant nucleic acid construct. An exogenous nucleic acid can also be a sequence that is native to an organism and that has been reintroduced into cells of that organism. An exogenous nucleic acid that includes a native sequence can often be distinguished from the naturally occurring sequence by the presence of non-natural sequences linked to the exogenous nucleic acid, e.g., non-native regulatory sequences flanking a native sequence in a recombinant nucleic acid construct. In addition, stably transformed exogenous nucleic acids typically are integrated at positions other than the position where the native sequence is found. It will be appreciated that an exogenous nucleic acid may have been introduced into a progenitor and not into the cell under consideration. For example, a transgenic plant containing an exogenous nucleic acid can be the progeny of a cross between a stably transformed plant and a non-transgenic plant. Such progeny are considered to contain the exogenous nucleic acid.

Recombinant constructs are also provided herein and can be used to transform plants or plant cells in order to modulate nitrogen levels. A recombinant nucleic acid construct comprises a nucleic acid encoding a nitrogen-modulating polypeptide as described herein, operably linked to a regulatory region suitable for expressing the nitrogen-modulating polypeptide in the plant or cell. Thus, a nucleic acid can comprise a nucleotide sequence that encodes any of the nitrogen-modulating polypeptides as set forth in SEQ ID NO:2, SEQ ID NOs:4-18, and the consensus sequence set forth in FIG. 1.

Vectors containing nucleic acids such as those described herein also are provided. A “vector” is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. Suitable vector backbones include, for example, those routinely used in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs, or PACs. The term “vector” includes cloning and expression vectors, as well as viral vectors and integrating vectors. An “expression vector” is a vector that includes a regulatory region. Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, and retroviruses. Numerous vectors and expression systems are commercially available from such corporations as Novagen (Madison, Wis.), Clontech (Palo Alto, Calif.), Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies (Carlsbad, Calif.).

The vectors provided herein also can include, for example, origins of replication, scaffold attachment regions (SARs), and/or markers. A marker gene can confer a selectable phenotype on a plant cell. For example, a marker can confer biocide resistance, such as resistance to an antibiotic (e.g., kanamycin, G418, bleomycin, or hygromycin), or an herbicide (e.g., chlorosulfuron or phosphinothricin). In addition, an expression vector can include a tag sequence designed to facilitate manipulation or detection (e.g., purification or localization) of the expressed polypeptide. Tag sequences, such as green fluorescent protein (GFP), glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, or Flag™ tag (Kodak, New Haven, Conn.) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide, including at either the carboxyl or amino terminus.

Regulatory Regions

The term “regulatory region” refers to nucleotide sequences that influence transcription or translation initiation and rate, and stability and/or mobility of a transcription or translation product. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5′ and 3′ untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, and introns.

As used herein, the term “operably linked” refers to positioning of a regulatory region and a sequence to be transcribed in a nucleic acid so as to allow or facilitate transcription of such a sequence. For example, to bring a coding sequence under the control of a promoter, the translation initiation site of the translational reading frame of the polypeptide is typically positioned between one and about fifty nucleotides downstream of the promoter. A promoter can, however, be positioned as much as about 5,000 nucleotides upstream of the translation initiation site, or about 2,000 nucleotides upstream of the transcription start site. A promoter typically comprises at least a core (basal) promoter. A promoter also may include at least one control element, such as an enhancer sequence, an upstream element or an upstream activation region (UAR). For example, a suitable enhancer is a cis-regulatory element (−212 to −154) from the upstream region of the octopine synthase (ocs) gene. Fromm et al., The Plant Cell 1:977-984 (1989). The choice of promoters to be included depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and cell- or tissue-preferential expression. It is a routine matter for one of skill in the art to modulate the expression of a coding sequence by appropriately selecting and positioning promoters and other regulatory regions relative to the coding sequence.

Some suitable promoters initiate transcription only, or predominantly, in certain cell types. For example, a promoter that is active predominantly in a reproductive tissue (e.g., fruit, ovule, pollen, pistils, female gametophyte, egg cell, central cell, nucellus, suspensor, synergid cell, flowers, embryonic tissue, embryo sac, embryo, zygote, endosperm, integument, or seed coat) can be used. Thus, as used herein a cell type- or tissue-preferential promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other cell types or tissues as well. Methods for identifying and characterizing promoter regions in plant genomic DNA include, for example, those described in the following references: Jordano, et al., Plant Cell, 1:855-866 (1989); Bustos, et al., Plant Cell, 1:839-854 (1989); Green, et al., EMBO J. 7, 4035-4044 (1988); Meier, et al., Plant Cell, 3, 309-316 (1991); and Zhang, et al., Plant Physiology 110: 1069-1079 (1996).

Examples of various classes of promoters are described below. Some of the promoters indicated below are described in more detail in U.S. Patent Application Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869; 60/583,691; 60/619,181; 60/637,140; 10/950,321; 10/957,569; 11/058,689; 11/172,703; 11/208,308; and PCT/US05/23639. It will be appreciated that a promoter may meet criteria for one classification based on its activity in one plant species, and yet meet criteria for a different classification based on its activity in another plant species. Nucleotide sequences of promoters are set forth in SEQ ID NOs:19-25.

Broadly Expressing Promoters

A promoter can be said to be “broadly expressing” when it promotes transcription in many, but not necessarily all, plant tissues. For example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the shoot, shoot tip (apex), and leaves, but weakly or not at all in tissues such as roots or stems. As another example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the stem, shoot, shoot tip (apex), and leaves, but can promote transcription weakly or not at all in tissues such as reproductive tissues of flowers and developing seeds. Non-limiting examples of broadly expressing promoters that can be included in the nucleic acid constructs provided herein include the p326 (SEQ ID NO:19), YP0144 (SEQ ID NO:20), YP0190 (SEQ ID NO:21), p13879 (SEQ ID NO:22), YP0050 (SEQ ID NO:23), p32449 (SEQ ID NO:24), 21876 (SEQ ID NO:25), YP0158, YP0214, YP0380, PT0848, and PT0633 promoters. Additional examples include the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived from T-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, and ubiquitin promoters such as the maize ubiquitin-1 promoter. In some cases, the CaMV 35S promoter is excluded from the category of broadly expressing promoters.

Root Promoters

Root-active promoters confer transcription in root tissue, e.g., root endodermis, root epidermis, or root vascular tissues. In some embodiments, root-active promoters are root-preferential promoters, i.e., confer transcription only or predominantly in root tissue. Root-preferential promoters include the YP0128, YP0275, PT0625, PT0660, PT0683, and PT0758 promoters. Other root-preferential promoters include the PT0613, PT0672, PT0678, PT0688, and PT0837 promoters, which drive transcription primarily in root tissue and to a lesser extent in ovules and/or seeds. Other examples of root-preferential promoters include the root-specific subdomains of the CaMV 35S promoter (Lam et al., Proc. Natl. Acad. Sci. USA 86:7890-7894 (1989)), root cell specific promoters reported by Conkling et al., Plant Physiol. 93:1203-1211 (1990), and the tobacco RD2 gene promoter.

Maturing Endosperm Promoters

In some embodiments, promoters that drive transcription in maturing endosperm can be useful. Transcription from a maturing endosperm promoter typically begins after fertilization and occurs primarily in endosperm tissue during seed development and is typically highest during the cellularization phase. Most suitable are promoters that are active predominantly in maturing endosperm, although promoters that are also active in other tissues can sometimes be used. Non-limiting examples of maturing endosperm promoters that can be included in the nucleic acid constructs provided herein include the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter (Bustos et al., Plant Cell 1(9):839-853 (1989)), the soybean trypsin inhibitor promoter (Riggs et al., Plant Cell 1(6):609-621 (1989)), the ACP promoter (Baerson et al., Plant Mol Biol, 22(2):255-267 (1993)), the stearoyl-ACP desaturase gene (Slocombe et al., Plant Physiol 104(4):167-176 (1994)), the soybean α subunit of β-conglycinin promoter (Chen et al., Proc Natl Acad Sci USA 83:8560-8564 (1986)), the oleosin promoter (Hong et al., Plant Mol Biol 34(3):549-555 (1997)), and zein promoters, such as the 15 kD zein promoter, the 16 kD zein promoter, 19 kD zein promoter, 22 kD zein promoter and 27 kD zein promoter. Also suitable are the Osgt-1 promoter from the rice glutelin-1 gene (Zheng et al., Mol. Cell. Biol. 13:5829-5842 (1993)), the beta-amylase gene promoter, and the barley hordein gene promoter. Other maturing endosperm promoters include the YP0092, PT0676, and PT0708 promoters.

Ovary Tissue Promoters

Promoters that are active in ovary tissues such as the ovule wall and mesocarp can also be useful, e.g., a polygalacturonidase promoter, the banana TRX promoter, and the melon actin promoter.

Embryo Sac/Early Endosperm Promoters

To achieve expression in embryo sac/early endosperm, regulatory regions can be used that are active in polar nuclei and/or the central cell, or in precursors to polar nuclei, but not in egg cells or precursors to egg cells. Most suitable are promoters that drive expression only or predominantly in polar nuclei or precursors thereto and/or the central cell. A pattern of transcription that extends from polar nuclei into early endosperm development can also be found with embryo sac/early endosperm-preferential promoters, although transcription typically decreases significantly in later endosperm development during and after the cellularization phase. Expression in the zygote or developing embryo typically is not present with embryo sac/early endosperm promoters.

Promoters that may be suitable include those derived from the following genes; Arabidopsis viviparous-1 (see, GenBank No. U93215); Arabidopsis atmycl (see, Urao (1996) Plant Mol. Biol., 32:571-57; Conceicao (1994) Plant, 5:493-505); Arabidopsis F1E (GenBank No. AF129516); Arabidopsis MEA; Arabidopsis FIS2 (GenBank No. AF096096); and F1E 1.1 (U.S. Pat. No. 6,906,244). Other promoters that may be suitable include those derived from the following genes: maize MAC1 (see, Sheridan (1996) Genetics, 142:1009-1020); maize Cat3 (see, GenBank No. L05934; Abler (1993) Plant Mol. Biol., 22:10131-1038). Other promoters include the following Arabidopsis promoters: YP0039, YP0101, YP1002, YP0110, YP0117, YP0119, YP0137, DME, YP0285, and YP0212. Other promoters that may be useful include the following rice promoters: p530c10, pOsFIE2-2, pOsMEA, pOsYp102, and pOsYp285.

Embryo Promoters

Regulatory regions that preferentially drive transcription in zygotic cells following fertilization can provide embryo-preferential expression. Most suitable are promoters that preferentially drive transcription in early stage embryos prior to the heart stage, but expression in late stage and maturing embryos is also suitable. Embryo-preferential promoters include the barley lipid transfer protein (Ltp1) promoter (Plant Cell Rep (2001) 20:647-654).

Photosynthetically Active Tissue Promoters

Photosynthetically active tissue promoters confer transcription in photosynthetically active tissue such as leaves and stems. Most suitable are promoters that drive expression only or predominantly such tissues. Examples of such promoters include the ribulose-1,5-bisphosphate carboxylase (RbcS) promoters such as the RbcS promoter from eastern larch (Larix laricina), the pine cab6 promoter (Yamamoto et al., Plant Cell Physiol. 35:773-778 (1994)), the Cab-1 gene promoter from wheat (Fejes et al., Plant Mol. Biol. 15:921-932 (1990)), the CAB-1 promoter from spinach (Lubberstedt et al., Plant Physiol. 104:997-1006 (1994)), the cab1R promoter from rice (Luan et al., Plant Cell 4:971-981 (1992)), the pyruvate orthophosphate dikinase (PPDK) promoter from corn (Matsuoka et al., Proc Natl Acad. Sci. USA 90:9586-9590 (1993)), the tobacco Lhcb1*2 promoter (Cerdan et al., Plant Mol. Biol. 33:245-255 (1997)), the Arabidopsis thaliana SUC2 sucrose-H+ symporter promoter (Truemit et al., Planta 196:564-570 (1995)), and thylakoid membrane protein promoters from spinach (psaD, psaF, psae, PC, FNR, atpC, atpD, cab, rbcS).

Inducible Promoters

Inducible promoters confer transcription in response to external stimuli such as chemical agents or environmental stimuli. For example, inducible promoters can confer transcription in response to hormones such as giberellic acid or ethylene, or in response to light or drought.

Basal Promoters

A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a “TATA box” element that may be located between about 15 and about 35 nucleotides upstream from the site of transcription initiation. Basal promoters also may include a “CCAAT box” element (typically the sequence CCAAT) and/or a GGGCG sequence, which can be located between about 40 and about 200 nucleotides, typically about 60 to about 120 nucleotides, upstream from the transcription start site.

Other Promoters

Other classes of promoters include, but are not limited to, leaf-preferential, stem/shoot-preferential, callus-preferential, and senescence-preferential promoters. Promoters designated YP0086, YP0188, YP0263, PT0758, PT0743, PT0829, YP0119, and YP0096, as described in the above-referenced patent applications, may also be useful.

Other Regulatory Regions

A 5′ untranslated region (UTR) can be included in nucleic acid constructs described herein. A 5′ UTR is transcribed, but is not translated, and lies between the start site of the transcript and the translation initiation codon and may include the +1 nucleotide. A 3′ UTR can be positioned between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA stability or attenuating translation. Examples of 3′ UTRs include, but are not limited to, polyadenylation signals and transcription termination sequences, e.g., a nopaline synthase termination sequence.

It will be understood that more than one regulatory region may be present in a recombinant polynucleotide, e.g., introns, enhancers, upstream activation regions, transcription terminators, and inducible elements. Thus, more than one regulatory region can be operably linked to the sequence of a polynucleotide encoding a carbon-modulating polypeptide.

Transgenic Plants and Plant Cells

The invention also features transgenic plant cells and plants comprising at least one recombinant nucleic acid construct described herein. A plant or plant cell can be transformed by having a construct integrated into its genome, i.e., can be stably transformed. Stably transformed cells typically retain the introduced nucleic acid with each cell division. A plant or plant cell can also be transiently transformed such that the construct is not integrated into its genome. Transiently transformed cells typically lose all or some portion of the introduced nucleic acid construct with each cell division such that the introduced nucleic acid cannot be detected in daughter cells after a sufficient number of cell divisions. Both transiently transformed and stably transformed transgenic plants and plant cells can be useful in the methods described herein.

Transgenic plant cells used in methods described herein can constitute part or all of a whole plant. Such plants can be grown in a manner suitable for the species under consideration, either in a growth chamber, a greenhouse, or in a field. Transgenic plants can be bred as desired for a particular purpose, e.g., to introduce a recombinant nucleic acid into other lines, to transfer a recombinant nucleic acid to other species, or for further selection of other desirable traits. Alternatively, transgenic plants can be propagated vegetatively for those species amenable to such techniques. Progeny include descendants of a particular plant or plant line. Progeny of an instant plant include seeds formed on F₁, F₂, F₃, F₄, F₅, F₆ and subsequent generation plants, or seeds formed on BC₁, BC₂, BC₃, and subsequent generation plants, or seeds formed on F₁BC₁, F₁BC₂, F₁BC₃, and subsequent generation plants. The designation F₁ refers to the progeny of a cross between two parents that are genetically distinct. The designations F₂, F₃, F₄, F₅ and F₆ refer to subsequent generations of self- or sib-pollinated progeny of an F₁ plant. Seeds produced by a transgenic plant can be grown and then selfed (or outcrossed and selfed) to obtain seeds homozygous for the nucleic acid construct.

Transgenic plants can be grown in suspension culture, or tissue or organ culture. For the purposes of this invention, solid and/or liquid tissue culture techniques can be used. When using solid medium, transgenic plant cells can be placed directly onto the medium or can be placed onto a filter that is then placed in contact with the medium. When using liquid medium, transgenic plant cells can be placed onto a flotation device, e.g., a porous membrane that contacts the liquid medium. Solid medium typically is made from liquid medium by adding agar. For example, a solid medium can be Murashige and Skoog (MS) medium containing agar and a suitable concentration of an auxin, e.g., 2,4-dichlorophenoxyacetic acid (2,4-D), and a suitable concentration of a cytokinin, e.g., kinetin.

When transiently transformed plant cells are used, a reporter sequence encoding a reporter polypeptide having a reporter activity can be included in the transformation procedure and an assay for reporter activity or expression can be performed at a suitable time after transformation. A suitable time for conducting the assay typically is about 1-21 days after transformation, e.g., about 1-14 days, about 1-7 days, or about 1-3 days. The use of transient assays is particularly convenient for rapid analysis in different species, or to confirm expression of a heterologous nitrogen-modulating polypeptide whose expression has not previously been confirmed in particular recipient cells.

Techniques for introducing nucleic acids into monocotyledonous and dicotyledonous plants are known in the art, and include, without limitation, Agrobacterium-mediated transformation, viral vector-mediated transformation, electroporation and particle gun transformation, e.g., U.S. Pat. Nos. 5,538,880; 5,204,253; 6,329,571 and 6,013,863. If a cell or cultured tissue is used as the recipient tissue for transformation, plants can be regenerated from transformed cultures if desired, by techniques known to those skilled in the art.

Plant Species

The polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, including dicots such as alfalfa, amaranth, apple, beans (including kidney beans, lima beans, dry beans, green beans), broccoli, cabbage, carrot, castor bean, cherry, chick peas, chicory, clover, cocoa, coffee, cotton, crambe, flax, grape, grapefruit, lemon, lentils, lettuce, linseed, mango, melon (e.g., watermelon, cantaloupe), mustard, orange, peach, peanut, pear, peas, pepper, plum, potato, oilseed rape, rapeseed (high erucic acid and canola), safflower, sesame, soybean, spinach, strawberry, sugar beet, sunflower, sweet potatoes, tea, tomato, and yams, as well as monocots such as banana, barley, bluegrass, date palm, fescue, field corn, garlic, millet, oat, oil palm, onion, pineapple, popcorn, rice, rye, ryegrass, sorghum, sudangrass, sugarcane, sweet corn, switchgrass, timothy, and wheat. Brown seaweeds, green seaweeds, red seaweeds, and microalgae can also be used.

Thus, the methods and compositions described herein can be used with dicotyledonous plants belonging, for example, to the orders Apiales, Arecales, Aristochiales, Asterales, Batales, Campanulales, Capparales, Caryophyllales, Casuarinales, Celastrales, Cornales, Cucurbitales, Diapensales, Dilleniales, Dipsacales, Ebenales, Ericales, Eucomiales, Euphorbiales, Fabales, Fagales, Gentianales, Geraniales, Haloragales, Hamamelidales, Illiciales, Juglandales, Lamiales, Laurales, Lecythidales, Leitneriales, Linales, Magniolales, Malvales, Myricales, Myrtales, Nymphaeales, Papaverales, Piperales, Plantaginales, Plumbaginales, Podostemales, Polemoniales, Potvgalales, Polygonales, Primulales, Proteales, Rafflesiales, Ranunculales, Rhamnales, Rosales, Rubiales, Salicales, Santales, Sapindales, Sarraceniaceae, Scrophulariales, Solanales, Trochodendrales, Theales, Umbellales, Urticales, and Violales. The methods and compositions described herein also can be utilized with monocotyledonous plants such as those belonging to the orders Alismatales, Arales, Arecales, Asparagales, Bromeliales, Commelinales, Cyclanthales, Cyperales, Eriocaulales, Hydrocharitales, Juncales, Liliales, Najadales, Orchidales, Pandanales, Poales, Restionales, Triuridales, Typhales, Zingiberales, and with plants belonging to Gymnospermae, e.g., Cycadales, Ginkgoales, Gnetales, and Pinales.

The methods and compositions can be used over a broad range of plant species, including species from the dicot genera Amaranthus, Arachis, Brassica, Calendula, Camellia, Capsicum, Carthamus, Cicer, Cichorium, Cinnamomum, Citrus, Citrullus, Coffea, Crambe, Cucumis, Cucurbita, Daucus, Dioscorea, Fragaria, Glycine, Gossypium, Helianthus, Lactuca, Lens, Linum, Lycopersicon, Malus, Mangifera, Medicago, Mentha, Nicotiana, Ocimum, Olea, Phaseolus, Pistacia, Pisum, Prunus, Pyrus, Rosmarinus, Salvia, Sesamum, Solanum, Spinacia, Theobroma, Thymus, Trifolium, Vaccinium, Vigna, and Vitis; and the monocot genera Allium, Ananas, Asparagus, Avena, Curcuma, Elaeis, Festuca, Hordeum, Lemna, Lolium, Musa, Oryza, Panicum, Pennisetum, Phleum, Poa, Saccharum, Secale, Sorghum, Triticosecale, Triticum, and Zea.

The methods and compositions described herein also can be used with brown seaweeds, e.g., Ascophyllum nodosum, Fucus vesiculosus, Fucus serratus, Himanthalia elongata, and Undaria pinnatifida; red seaweeds, e.g., Chondrus crispus, Cracilaria verrucosa, Porphyra umbilicalis, and Palmaria paimata; green seaweeds, e.g., Enteromorpha spp. and Ulva spp.; and microalgae, e.g., Spirulina spp. (S. platensis and S. maxima) and Odontella aurita. In addition, the methods and compositions can be used with Crypthecodinium cohnii, Schizochytriuni spp., and Haeniatococcus pluvialis.

In some embodiments, a plant is a member of the species Ananus comosus, Brassica campestris, Brassica napus, Brassica oleracea, Glycine max, Gossypium spp., Lactuca sativa, Lycopersicon esculentum, Musa paradisiaca, Oryza sativa, Solanum tuberosum, Triticum aestivum, Vitis vinifera, or Zea mays.

Methods of Inhibiting Expression of Nitrogen-Modulating Polypeptides

The polynucleotides and recombinant vectors described herein can be used to express or inhibit expression of a nitrogen-modulating polypeptide in a plant species of interest. The term “expression” refers to the process of converting genetic information of a polynucleotide into RNA through transcription, which is catalyzed by an enzyme, RNA polymerase, and into protein, through translation of mRNA on ribosomes. “Up-regulation” or “activation” refers to regulation that increases the production of expression products (mRNA, polypeptide, or both) relative to basal or native states, while “down-regulation” or “repression” refers to regulation that decreases production of expression products (mRNA, polypeptide, or both) relative to basal or native states.

A number of nucleic-acid based methods, including anti-sense RNA, ribozyme directed RNA cleavage, and interfering RNA (RNAi) can be used to inhibit protein expression in plants. Antisense technology is one well-known method. In this method, a nucleic acid segment from the endogenous gene is cloned and operably linked to a promoter so that the antisense strand of RNA is transcribed. The recombinant vector is then transformed into plants, as described above, and the antisense strand of RNA is produced. The nucleic acid segment need not be the entire sequence of the endogenous gene to be repressed, but typically will be substantially identical to at least a portion of the endogenous gene to be repressed. Generally, higher homology can be used to compensate for the use of a shorter sequence. Typically, a sequence of at least 30 nucleotides is used (e.g., at least 40, 50, 80, 100, 200, 500 nucleotides or more).

Thus, for example, an isolated nucleic acid provided herein can be an antisense nucleic acid to one of the aforementioned nucleic acids encoding a nitrogen-modulating polypeptide, e.g., SEQ ID NO:2, SEQ ID NOs:4-18, or the consensus sequence set forth in FIG. 1. A nucleic acid that decreases the level of a transcription or translation product of a gene encoding a nitrogen-modulating polypeptide is transcribed into an antisense nucleic acid similar or identical to the sense coding sequence of the nitrogen-modulating polypeptide. Alternatively, the transcription product of an isolated nucleic acid can be similar or identical to the sense coding sequence of a nitrogen-modulating polypeptide, but is an RNA that is unpolyadenylated, lacks a 5′ cap structure, or contains an unsplicable intron.

In another method, a nucleic acid can be transcribed into a ribozyme, or catalytic RNA, that affects expression of an mRNA. (See, U.S. Pat. No. 6,423,885). Ribozymes can be designed to specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. Heterologous nucleic acids can encode ribozymes designed to cleave particular mRNA transcripts, thus preventing expression of a polypeptide. Hammerhead ribozymes are useful for destroying particular mRNAs, although various ribozymes that cleave mRNA at site-specific recognition sequences can be used. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target RNA contain a 5′-UG-3′ nucleotide sequence. The construction and production of hammerhead ribozymes is known in the art. See, for example, U.S. Pat. No. 5,254,678 and WO 02/46449 and references cited therein. Hammerhead ribozyme sequences can be embedded in a stable RNA such as a transfer RNA (tRNA) to increase cleavage efficiency in vivo. Perriman, et al., Proc. Natl. Acad. Sci. USA, 92(13):6175-6179 (1995); de Feyter and Gaudron, Methods in Molecular Biology, Vol. 74, Chapter 43, “Expressing Ribozymes in Plants”, Edited by Turner, P. C, Humana Press Inc., Totowa, N.J. RNA endoribonucleases such as the one that occurs naturally in Tetrahymena thermophila, and which have been described extensively by Cech and collaborators can be useful. See, for example, U.S. Pat. No. 4,987,071.

Methods based on RNA interference (RNAi) can be used. RNA interference is a cellular mechanism to regulate the expression of genes and the replication of viruses. This mechanism is thought to be mediated by double-stranded small interfering RNA molecules. A cell responds to such a double-stranded RNA by destroying endogenous mRNA having the same sequence as the double-stranded RNA. Methods for designing and preparing interfering RNAs are known to those of skill in the art; see, e.g., WO 99/32619 and WO 01/75164. For example, a construct can be prepared that includes a sequence that is transcribed into an interfering RNA. Such an RNA can be one that can anneal to itself, e.g., a double stranded RNA having a stem-loop structure. One strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sense coding sequence of the polypeptide of interest, and that is from about 10 nucleotides to about 2,500 nucleotides in length. The length of the sequence that is similar or identical to the sense coding sequence can be from 10 nucleotides to 500 nucleotides, from 15 nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides, or from 25 nucleotides to 100 nucleotides. The other strand of the stem portion of a double stranded RNA comprises an antisense sequence of the nitrogen-modulating polypeptide of interest, and can have a length that is shorter, the same as, or longer than the corresponding length of the sense sequence. The loop portion of a double stranded RNA can be from 10 nucleotides to 5,000 nucleotides, e.g., from 15 nucleotides to 1,000 nucleotides, from 20 nucleotides to 500 nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portion of the RNA can include an intron. See, e.g., WO 99/53050.

In some nucleic-acid based methods for inhibition of gene expression in plants, a suitable nucleic acid can be a nucleic acid analog. Nucleic acid analogs can be modified at the base moiety, sugar moiety, or phosphate backbone to improve, for example, stability, hybridization, or solubility of the nucleic acid. Modifications at the base moiety include deoxyuridine for deoxythymidine, and 5-methyl-2′-deoxycytidine and 5-bromo-2′-deoxycytidine for deoxycytidine. Modifications of the sugar moiety include modification of the 2′ hydroxyl of the ribose sugar to form 2′-O-methyl or 2′-O-allyl sugars. The deoxyribose phosphate backbone can be modified to produce morpholino nucleic acids, in which each base moiety is linked to a six-membered morpholino ring, or peptide nucleic acids, in which the deoxyphosphate backbone is replaced by a pseudopeptide backbone and the four bases are retained. See, for example, Summerton and Weller, 1997, Antisense Nucleic Acid Drug Dev., 7:187-195; Hyrup et al., 1996, Bioorgan. Med. Chem., 4: 5-23. In addition, the deoxyphosphate backbone can be replaced with, for example, a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite, or an alkyl phosphotriester backbone.

Transgenic Plant Phenotypes

A transformed cell, callus, tissue, or plant can be identified and isolated by selecting or screening the engineered plant material for particular traits or activities, e.g., those encoded by marker genes or antibiotic resistance genes. Such screening and selection methodologies are well known to those having ordinary skill in the art. In addition, physical and biochemical methods can be used to identify transformants. These include Southern analysis or PCR amplification for detection of a polynucleotide; Northern blots, S1 RNase protection, primer-extension, or RT-PCR amplification for detecting RNA transcripts; enzymatic assays for detecting enzyme or ribozyme activity of polypeptides and polynucleotides; and protein gel electrophoresis, Western blots, immunoprecipitation, and enzyme-linked immunoassays to detect polypeptides. Other techniques such as in situ hybridization, enzyme staining, and immunostaining also can be used to detect the presence or expression of polypeptides and/or polynucleotides. Methods for performing all of the referenced techniques are well known.

Transgenic plants can have an altered phenotype as compared to a corresponding control plant that either lacks the transgene or does not express the transgene. A polypeptide can affect the phenotype of a plant (e.g., a transgenic plant) when expressed in the plant, e.g., at the appropriate time(s), in the appropriate tissue(s), or at the appropriate expression levels. Phenotypic effects can be evaluated relative to a control plant that does not express the exogenous polynucleotide of interest, such as a corresponding wild type plant, a corresponding plant that is not transgenic for the exogenous polynucleotide of interest but otherwise is of the same genetic background as the transgenic plant of interest, or a corresponding plant of the same genetic background in which expression of the polypeptide is suppressed, inhibited, or not induced (e.g., where expression is under the control of an inducible promoter). A plant can be said “not to express” a polypeptide when the plant exhibits less than 10%, e.g., less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.01%, or 0.001%, of the amount of polypeptide or mRNA encoding the polypeptide exhibited by the plant of interest. Expression can be evaluated using methods including, for example, RT-PCR, Northern blots, S1 RNase protection, primer extensions, Western blots, protein gel electrophoresis, immunoprecipitation, enzyme-linked immunoassays, chip assays, and mass spectrometry. It should be noted that if a polypeptide is expressed under the control of a tissue-specific or broadly expressing promoter, expression can be evaluated in the entire plant or in a selected tissue. Similarly, if a polypeptide is expressed at a particular time, e.g., at a particular time in development or upon induction, expression can be evaluated selectively at a desired time period.

In some embodiments, a plant in which expression of a nitrogen-modulating polypeptide is modulated can have increased levels of seed nitrogen. For example, a nitrogen-modulating polypeptide described herein can be expressed in a transgenic plant, resulting in increased levels of seed nitrogen. The seed nitrogen level can be increased by at least 5 percent, e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more than 100 percent, as compared to the seed nitrogen level in a corresponding control plant that does not express the transgene. In some embodiments, a plant in which expression of a nitrogen-modulating polypeptide is modulated can have decreased levels of seed nitrogen. The seed nitrogen level can be decreased by at least 5 percent, e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or more than 50 percent, as compared to the seed nitrogen level in a corresponding control plant that does not express the transgene.

Plants for which modulation of levels of seed nitrogen can be useful include, without limitation, alfalfa, lettuce, carrot, onion, broccoli, tomato, potato, sugarcane, grape, cotton, canola, sweet corn, popcorn, field corn, peas, beans, safflower, soybean, coffee, amaranth, rapeseed, peanut, sunflower, oil palm, wheat, rye, barley, oat, rice, millet, strawberry, pineapple, melon, peach, pear, apple, cherry, orange, lemon, grapefruit, plum, mango, banana, fescue, ryegrass, bluegrass, clover, timothy, sudangrass, switchgrass and sorghum. Increases in seed nitrogen in such plants can provide improved nutritional content in geographic locales where dietary intake of protein/amino acid is often insufficient. Decreases in seed nitrogen in such plants can be useful in situations where seeds are not the primary plant part that is harvested for human or animal consumption.

In some embodiments, a plant in which expression of a nitrogen-modulating polypeptide is modulated can have increased or decreased levels of nitrogen in one or more non-seed tissues, e.g., leaf tissues, stem tissues, root or corm tissues, or fruit tissues other than seed. For example, the nitrogen level can be increased by at least 5 percent, e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more than 100 percent, as compared to the nitrogen level in a corresponding control plant that does not express the transgene. In some embodiments, a plant in which expression of a nitrogen-modulating polypeptide is modulated can have decreased levels of nitrogen in one or more non-seed tissues. The nitrogen level can be decreased by at least 5 percent, e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or more than 50 percent as compared to the nitrogen level in a corresponding control plant that does not express the transgene.

Plants for which modulation of levels of nitrogen in non-seed tissues can be useful include, without limitation, alfalfa, lettuce, carrot, onion, broccoli, tomato, potato, sugarcane, grape, sweet corn, popcorn, field corn, peas, beans, safflower, soybean, coffee, amaranth, rapeseed, peanut, sunflower, oil palm, wheat, rye, barley, oat, rice, millet, strawberry, pineapple, melon, peach, pear, apple, cherry, orange, lemon, grapefruit, plum, mango, banana, fescue, ryegrass, bluegrass, clover, timothy, sudangrass, switchgrass and sorghum.

Increases in non-seed nitrogen in such plants can provide improved nutritional content in edible fruits and vegetables, or improved animal forage. Decreases in non-seed nitrogen can provide more efficient partitioning of nitrogen to plant part(s) that are harvested for human or animal consumption.

Typically, a difference (e.g., an increase) in the amount of nitrogen in a transgenic plant or cell relative to a control plant or cell is considered statistically significant at p<0.05 with an appropriate parametric or non-parametric statistic, e.g., Chi-square test, Student's t-test, Mann-Whitney test, or F-test. In some embodiments, a difference in the amount of nitrogen is statistically significant at p<0.01, p<0.005, or p<0.001. A statistically significant difference in, for example, the amount of nitrogen in seeds of a transgenic plant compared to the amount in cells of a control plant indicates that (1) the recombinant nucleic acid present in the transgenic plant results in altered nitrogen levels and/or (2) the recombinant nucleic acid warrants further study as a candidate for altering the amount of nitrogen in a plant.

Articles of Manufacture

Also provided herein are articles of manufacture that can include, for example, a mixture of seeds (e.g., a substantially uniform mixture of seeds) from the transgenic plants provided herein. The seed mixture can be conditioned and packaged using means known in the art to prepare an article of manufacture. A package of seed can have a label e.g., a tag or label secured to the packaging material, a label printed on the packaging material or a label inserted within the package. The label can indicate that plants grown from the seeds contained within the package can produce a crop having a higher level of seed nitrogen relative to corresponding control plants.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Transgenic Plants

The following symbols are used in the Examples: T₁: first generation transformant; T₂: second generation, progeny of self-pollinated T₁ plants; T₃: third generation, progeny of self-pollinated T₂ plants; T₄: fourth generation, progeny of self-pollinated T₃ plants. Independent transformations are referred to as events.

The following nucleic acids were isolated from Arabidopsis thaliana ecotype Wassilewskija (Ws) plants. Ceres cDNA ID 2998984 (SEQ ID NO:1) is a genomic DNA clone that is predicted to encode a 505 amino acid (SEQ ID NO:2) putative oligopeptide transporter polypeptide. Ceres clone 117581 (cDNA ID 23364185; SEQ ID NO:3) is a cDNA clone that is predicted to encode a 587 amino acid (SEQ ID NO:4) putative peptide transporter polypeptide.

Each isolated polynucleotide described above was cloned into a vector containing a phosphinothricin acetyltransferase gene, which confers Finale™ resistance to transformed plants. NB42-35S binary vectors were constructed that contained Ceres cDNA ID 2998984 or Ceres clone 117581 operably linked to the cauliflower mosaic virus (CaMV) 35S regulatory region. The NB42-35S binary vector is a derivative of the pMOG800 binary vector.

Wild-type Arabidopsis thaliana ecotype C24 plants were transformed separately with each NB42-35S binary vector containing Ceres cDNA ID 2998984 or Ceres clone 117581. The transformations were performed essentially as described in Bechtold et al., C.R. Acad. Sci. Paris, 316:1194-1199 (1993).

Transgenic Arabidopsis lines containing Ceres cDNA ID 2998984 or Ceres clone 117581 were designated SR00829 and SR05001, respectively. The presence of the Ceres cDNA ID 2998984 vector in SR00829 and the Ceres clone 117581 vector in SR05001 was confirmed by Finale™ resistance, polymerase chain reaction (PCR) amplification from green leaf tissue extract, and sequencing of PCR products. As controls for transgenic Arabidopsis ecotype C24 plants, wild-type Arabidopsis ecotype C24 plants were transformed with the empty vector NB42-35S.

The in planta nucleotide sequences of Ceres cDNA ID 2998984 and Ceres clone 117581 were compared to the homologous Arabidopsis ecotype Columbia sequences. The in planta nucleotide sequence of Ceres clone 117581 differed from the homologous Columbia sequence by one nucleotide. The in planta nucleotide sequence of Ceres cDNA ID 2998984 contained base pair insertions, deletions, and substitutions compared to the homologous Columbia sequence.

To determine if the overall structure of the predicted polypeptide encoded by Ceres cDNA ID 2998984 was similar to that of the predicted polypeptide encoded by the homologous Columbia nucleotide sequence, both sequences were analyzed for potential transmembrane domains characteristic of transporter polypeptides using the TMpred program (ch.embnet.org/software/TMPRED_form). The analysis indicated that both predicted polypeptides had the expected 12 transmembrane spanning regions. However, prediction of the translation initiation sites indicated that the predicted polypeptide encoded by Ceres cDNA ID 2998984 was 40 amino acids shorter at the amino terminus than the predicted polypeptide encoded by the Columbia homolog. Therefore, the predicted polypeptide encoded by Ceres cDNA ID 2998984 lacked the secretory signal peptide sequence contained in the first 40 amino acids of the predicted Columbia polypeptide sequence according to the SignalP algorithm (cbs.dtu.dk/services/SignalP/). Analysis of the predicted polypeptide sequence encoded by Ceres cDNA ID 2998984 using the iPSORT signal sequence prediction algorithm (hc.ims.u-tokyo.ac.jp/iPSORT/index.html#aaindex) indicated that the first 40 amino acids contained a potential chloroplast targeting signal sequence.

Transgenic Arabidopsis lines were screened as follows: 1) T₁ candidates in the greenhouse were screened for morphological phenotypes, 2) T₂ seeds were analyzed for carbon and nitrogen content, 3) increased carbon and/or nitrogen content was confirmed in T₃ seeds, and 4) T₂ plants were evaluated for negative phenotypes and Finale™ segregation.

Five events of each of SR00829 and SR05001 were screened for visible phenotypic alterations in the T₁ generation. The physical appearance of all of the T₁ plants was identical to that of the corresponding control plants.

Example 2 Analysis of Carbon and Nitrogen Content in Transgenic Arabidopsis Seeds

Approximately 2.00±0.15 mg of dried transgenic Arabidopsis seeds (about 100 seeds) were weighed into a tin cup and analyzed for total carbon and nitrogen content.

Three matched controls were prepared in a manner identical to the experimental samples and spaced evenly throughout the batch. The first three samples in every batch were a blank (empty tin cup), bypass, (approximately 5 mg of aspartic acid), and a standard (5.00±0.15 mg aspartic acid), respectively. Aspartic acid was weighed into a tin cup using an analytical balance. Blanks were entered between every 15 experimental samples.

Analysis was completed using a FlashEA 1112 NC Analyzer (Thermo Finnigan, San Jose, Calif.). The instrument parameters were as follows: left furnace 900° C., right furnace 840° C., oven 50° C., gas flow carrier 130 mL/min., and gas flow reference 100 mL/min. The data parameter LLOD was 0.25 mg for the standard and different for other materials. The data parameter LLOQ was 3 mg for the standard, 1 mg for seed tissue, and different for other materials.

Quantification was performed using EA 1112 software. The results were normalized and expressed in absolute percentages. Each sample was analyzed in triplicate, and the standard deviation was calculated. Non-transgenic controls were previously determined to have a total carbon content of 53.3±2.4% and a total nitrogen content of 3.9±0.3%. The deviation from theoretical of the aspartic acid standard was ±2.0% for carbon and ˜1.0% for nitrogen. To be declared valid, each run was required to have an aspartic acid (standard) weight of 5 mg±0.15 mg, and the blank(s) were required to have no recorded nitrogen or carbon content. The percent standard deviation between replicate samples was required to be below 10%.

Example 3 Results for SR00829 Events

T₂ and T₃ seeds from two events of SR00829 containing Ceres cDNA ID 2998984 were analyzed for total carbon and nitrogen content as described in Example 2.

The nitrogen content of T₂ seeds from two events of SR00829 was significantly increased compared to the nitrogen content of corresponding control seeds. As presented in Table 1, the nitrogen content was increased to 10% and 109% in seeds from events −01 and −02, respectively, compared to the nitrogen content in control seeds.

TABLE 1 Total nitrogen content (% control) of T₂ and T₃ seeds from SR00829 events Event -01 Event -02 Control T₂ 110 ± 1 109 ± 2 100 ± 1 p-value 0.001 0.002 NA T₃ 111 ± 3 118 ± 5 100 ± 3 p-value <0.01  0.01  NA

The nitrogen content of T₃ seeds from two events of SR00829 was significantly increased compared to the nitrogen content of corresponding control seeds. As presented in Table 1, the nitrogen content was increased to 111% and 118% in seeds from events −01 and −02, respectively, compared to the nitrogen content in control seeds.

The carbon content of T₂ and T₃ seeds from SR00829 events was not observed to differ significantly from the carbon content of corresponding control seeds.

T₃ seeds from SR00829 events analyzed for carbon and nitrogen content were collected from one T₂ plant from each event.

The segregation of Finale™ resistance in T₂ plants from events −01 and −02 of SR00829 was a 3:1 ratio of resistant to sensitive.

There were no observable or statistically significant differences between T₂ SR00829 and control plants in germination, onset of flowering, rosette area, fertility, plant height, and general morphology/architecture.

Example 4 Results for SR05001 Events

T₂ and T₃ seeds from two events of SR05001 containing Ceres clone 117581 were analyzed for total carbon and nitrogen content as described in Example 2.

The carbon content of T₂ seeds from one event of SR05001 was significantly decreased compared to the carbon content of corresponding control seeds. As presented in Table 2, the carbon content was decreased to 97% in seeds from event −02 compared to the carbon content in control seeds.

TABLE 2 Total carbon content (% control) of T₂ and T₃ seeds from SR05001 events Event -02 Event -03 Control T₂  97 ± 2 102 ± 2 100 ± 1 p-value 0.03 0.14 NA T₃ 106 ± 1 107 ± 2 100 ± 2 p-value 0.01 0.01 NA

The nitrogen content of T₂ seeds from two events of SR05001 was significantly increased compared to the nitrogen content of corresponding control seeds. As presented in Table 3, the nitrogen content was increased to 112% and 115% in seeds from events −02 and −03, respectively, compared to the nitrogen content in control seeds.

TABLE 3 Total nitrogen content (% control) of T₂ and T₃ seeds from SR05001 events Event -02 Event -03 Control T₂ 112 ± 3 115 ± 1 100 ± 4 p-value <0.01 <0.01 NA T₃ 109 ± 1 106 ± 2 100 ± 2 p-value <0.01  0.02 NA

The carbon content of T₃ seeds from two events of SR05001 was significantly increased compared to the carbon content of corresponding control seeds. As presented in Table 2, the carbon content was increased to 106% and 107% in seeds from events −02 and −03, respectively, compared to the carbon content in control seeds.

The nitrogen content of T₃ seeds from two events of SR05001 was significantly increased compared to the nitrogen content of corresponding control seeds. As presented in Table 3, the nitrogen content was increased to 109% and 106% in seeds from events −02 and −03, respectively, compared to the nitrogen content in control seeds.

T₃ seeds from SR05001 events analyzed for carbon and nitrogen content were collected from one T₂ plant from each event.

The segregation of Finale™ resistance in T₂ plants from events −02 and −03 of SR05001 was a 3:1 ratio of resistant to sensitive.

There were no observable or statistically significant differences between T₂ SR05001 and control plants in germination, onset of flowering, rosette area, fertility, seed size, and general morphology/architecture.

Example 5 Determination of Functional Homolog and/or Ortholog Sequences

A subject sequence was considered a functional homolog or ortholog of a query sequence if the subject and query sequences encoded proteins having a similar function and/or activity. A process known as Reciprocal BLAST (Rivera et al., Proc. Natl. Acad. Sci. USA, 95:6239-6244 (1998)) was used to identify potential functional homolog and/or ortholog sequences from databases consisting of all available public and proprietary peptide sequences, including NR from NCBI and peptide translations from Ceres clones.

Before starting a Reciprocal BLAST process, a specific query polypeptide was searched against all peptides from its source species using BLAST in order to identify polypeptides having sequence identity of 80% or greater to the query polypeptide and an alignment length of 85% or greater along the shorter sequence in the alignment. The query polypeptide and any of the aforementioned identified polypeptides were designated as a cluster.

The main Reciprocal BLAST process consists of two rounds of BLAST searches; forward search and reverse search. In the forward search step, a query polypeptide sequence, “polypeptide A,” from source species SA was BLASTed against all protein sequences from a species of interest. Top hits were determined using an E-value cutoff of 10-5 and an identity cutoff of 35%. Among the top hits, the sequence having the lowest E-value was designated as the best hit, and considered a potential functional homolog or ortholog. Any other top hit that had a sequence identity of 80% or greater to the best hit or to the original query polypeptide was considered a potential functional homolog or ortholog as well. This process was repeated for all species of interest. In the reverse search round, the top hits identified in the forward search from all species were BLASTed against all protein sequences from the source species SA. A top hit from the forward search that returned a polypeptide from the aforementioned cluster as its best hit was also considered as a potential functional homolog or ortholog.

Functional homologs and/or orthologs were identified by manual inspection of potential functional homolog and/or ortholog sequences. Representative functional orthologs for SEQ ID NO:4 are shown in FIG. 1. The percent identities of functional orthologs to SEQ ID NO:4 are shown below in Table 4.

TABLE 4 Percent identity to Ceres clone 117581 (SEQ ID NO: 4) SEQ ID % Designation Species NO: Identity e-value CeresClone: 328378 Zea mays 5 70.4 0 gi|2655098 Hordeum vulgare 6 68.2 0 subsp. vulgare gi|34895718 Oryza sativa subsp. 7 68 0 japonica gi|50933627 Oryza sativa subsp. 8 64 0 japonica gi|4102839 Lycopersicon 9 63 0 esculentum gi|31088360 Vicia faba 10 62.9 0 gi|6635838 Prunus dulcis 11 61.4 0 gi|56784523 Oryza sativa subsp. 12 56.7 0 japonica gi|56784524 Oryza sativa subsp. 13 51.6 0 japonica gi|6409176 Oryza sativa 15 49.5 0 gi|50059161 Triticum aestivum 14 49.5 0 CeresClone: 352232 Zea mays 16 48.5 0 gi|33411520 Prunus persica 17 47.1 0 gi|31429847 Oryza sativa 18 47.1 0

OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A method of modulating the level of nitrogen in a plant, said method comprising introducing into a plant cell an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs:4-18, wherein a tissue of a plant produced from said plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid.
 2. The method of claim 1, wherein said difference is an increase in the level of nitrogen.
 3. The method of claim 1, wherein said isolated nucleic acid is operably linked to a regulatory region.
 4. The method of claim 3, wherein said regulatory region is a promoter selected from the group consisting of YP0092, PT0676, PT0708, PT0613, PT0672, PT0678, PT0688, PT0837, the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene promoter, the soybean α subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, and the barley hordein gene promoter.
 5. A method of producing a plant tissue, said method comprising growing a plant cell comprising an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs:4-18, wherein said tissue has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid.
 6. A plant cell comprising an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs:4-18, wherein a tissue of a plant produced from said plant cell has a difference in the level of nitrogen as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid.
 7. A transgenic plant comprising the plant cell of claim
 6. 8. Progeny of the plant of claim 7, wherein said progeny has a difference in the level of nitrogen as compared to the level of nitrogen in a corresponding control plant that does not comprise said isolated nucleic acid.
 9. Seed from a transgenic plant according to claim
 7. 10. Vegetative tissue from a transgenic plant according to claim
 7. 11. A food product comprising vegetative tissue from a transgenic plant according to claim
 7. 12. A feed product comprising vegetative tissue from a transgenic plant according to claim
 7. 